The "best" way to accomplish this is the way that works best for you.
In other words, there are several ways to do this, none (or all) of which are the "best." Asking which way is the "best" way is like asking which color is "best" -- red or blue? Green or yellow? Black or white?
As for one way to do it, you could set up a PPTP VPN on your Server 2003 box, then she would be able to VPN into the network and access shares as if she were sitting there on the local network.
There are plenty of guides (found with super-simple Google searches) on how to set up PPTP VPNs on Server 2003 (here's a hint: Routing and Remote Access).
Then it's just a matter of setting up the VPN connection on her MacBook Pro.
Another way to do it would be to open up the ports in your server's firewall to allow SMB (or whatever protocol you're using) access, then she could simply connect to the shares without having to go through a VPN. There are some inherent security risks with doing this, though.
Yet another way would be to allow FTP access, then she could work locally on her machine then upload the finished files to the server.
Which one of those is the "best" way is completely subjective and depends on a lot of factors about your setup and network. That would be up to you to decide, as no one here can tell you what works best for you.
